Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-03-11

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All times shown according to UTC.

Time Nick Message
00:38 kyanardag_ left #bioperl
03:52 CIA-57 bioperl6: takadonet master * rf572224 / (lib/Bio/Role/Location.pm lib/Bio/Role/Location/Simple.pm): Moved over most 'standard' attributes from Simple Role to Location Role. - http://bit.ly/hPz6MR
03:59 CIA-57 bioperl6: takadonet master * rf28b377 / lib/Bio/Role/Location/Fuzzy.pm : Fuzzy now using Bio::Role::Location for all attributes at the moment. Passing one more test - http://bit.ly/gNHkWy
04:05 CIA-57 bioperl6: takadonet master * r3ed911a / lib/Bio/Role/Location/Split.pm : Split now using Bio::Role::Location for most attributes - http://bit.ly/e498kp
04:47 CIA-57 bioperl-live: Chris Fields master * r8267ea5 / README : not using subversion - http://bit.ly/i7B8aX
05:08 CIA-57 bioperl-live: Chris Fields master * r82f72da / README : test redmine - http://bit.ly/eGH6x8
05:13 CIA-57 bioperl-live: Chris Fields master * r8c58519 / README : test redmine post-receive hook - http://bit.ly/gjnmlu
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13:03 takadonet morning all
13:32 andrei joined #bioperl
13:42 andrei hey guys, I'm trying to modify a genbank file, and save it under another name. When I save it it does not save the comments that are found in the original genbank file...
13:42 andrei here is the script https://gist.github.com/865885
14:00 andrei anyone here?
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14:02 takadonet andrei: hey
14:03 takadonet you have to be little patience here since most people are at work right nowp
14:03 takadonet also it's early morning for most as well
14:03 takadonet what do you mean by comments?
14:04 andrei well the COMMENT section in genbank
14:04 andrei in a genbank file sorry
14:04 takadonet hmm give me a sec
14:06 andrei also while running this code https://gist.github.com/865917 I can see the COMMENT section
14:07 andrei while running this one https://gist.github.com/865918 does not print the COMMENT section
14:07 takadonet you used basys for making your annotation?
14:08 andrei yes
14:08 takadonet cool
14:08 andrei isn't that good?
14:09 takadonet it is :)
14:10 andrei this happens on the genbank files from basys
14:11 andrei I tried the script with a genbank file from NCBI and it copied the COMMENT and all the others, exept for DBLINK
14:11 takadonet well the first code you posted worked for me using a standard genbank file from NCBI
14:11 takadonet the comment are still there
14:11 andrei yes
14:11 andrei for me too
14:11 andrei exept it did not copy DBLINK
14:12 andrei did it copy it for you?
14:13 takadonet it did not
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14:16 andrei and it doesn't seem to be stored in annotations either
14:16 andrei if you try to get dblink with get_Annotations it does not print anything
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14:25 kai I'd check the parser
14:25 kai haven't played with the genbank one much, but the embl parser has it's rough edges
14:35 andrei I think I figured it out...
14:36 andrei if a section in a genbank file is empty it is not stored in the annotation objecyt
14:36 andrei resulting in the loss of that section if you try to save it
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15:00 Ultini hi all, who do I need to contact/ask about submitting a module underneath the Bio:: namespace?
15:04 takadonet probably pyrimidine  which is  Chris Fields
15:04 Ultini okedoke
15:04 Ultini it's by no means ready yet
15:04 takadonet https://github.com/cjfields
15:04 Ultini thanks a lot :)
15:07 takadonet Ultini: np
15:17 perl_splut actually you shouldn't need to contact anyone unless you want it added to the bioperl distribution
15:17 perl_splut just try not to step on any already existing Bio:: objects...
15:24 dbolser Ultini: just be sure to write doc and tests, and it'll get accepted
15:24 pyrimidine Ultini: echoing what perl_splut said; we are actively encouraging new code as separate distributions on CPAN, as we are also actively pushing for modularizing our current code into more manageable bits
15:25 pyrimidine with the ultimate goal of creating an installer for any BioPerl-specific modules
15:26 pyrimidine rbuels: http://redmine.open-bio.org/​projects/bioperl/repository
15:26 Ultini well I'm a PhD student unde Julian Gough who runs supfam.org so I'm making a module for playing with our database
15:27 pyrimidine Ultini: nice!
15:27 rbuels pyrimidine: interesting.
15:27 pyrimidine I also agree with dbolser, in that docs ***and tests*** help
15:28 Ultini though I'm gunna have to have a public and a top-secret version of it :D
15:28 rbuels pyrimidine: slow.
15:28 pyrimidine rbuels: yeah, not sure about whether it's worth making public
15:28 dbolser Ultini: say hi to julian for me :D
15:28 Ultini not really sure how I could do lots of tests since you would need a mysql install of superfamily
15:28 rbuels pyrimidine: you mean the whole redmine? or the repository view
15:28 Ultini dbolser heh I will do when he gets back from South Africa
15:28 pyrimidine rbuels: repo view
15:29 rbuels pyrimidine: the github one is way better
15:29 dbolser Ultini: you could put some of supfam in an sqllte...
15:29 pyrimidine rbuels: it's sort of redundant with ... yes, exactly
15:29 * rbuels nods
15:29 Ultini dbolser: yeah that's not a bad idea
15:29 rbuels pyrimidine: is there any way to make the repository tab link to github?
15:29 rbuels that would be the ideal thing i think
15:30 * rbuels doesn't know how flexible redmine's conf is
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15:30 pyrimidine rbuels: worth looking into
15:30 pyrimidine rbuels: however, the hook is needed b/c we can now set up tagged commits
15:30 pyrimidine that link to bug reports, features, etc
15:30 rbuels ah, i see
15:30 rbuels yes
15:30 rbuels that's a big win
15:31 pyrimidine :)
15:31 rbuels i always liked that with trac + subversion
15:31 pyrimidine now, if we can only get the rest of the devs to follow that... :P
15:32 pyrimidine Ultini: does the code interact with the mysql db directly, or is it web-based?
15:33 Ultini directly
15:33 pyrimidine ok
15:33 Ultini it would be cool if I added stuff to fire up one of our public amazon ec2 images for you to use instead, but this is all a pipe dream
15:35 * Ultini better get back to work
15:35 pyrimidine we're (Open Bioinformatics Foundation) moving our resources off local servers to EC2 and other hosted services (GitHub for VC, etc).  http://redmine.open-bio.org/ is on EC2
15:36 Ultini yeah it makes things a lot easier if you can just request a ready installed machine than struggling to setup mysql with our honking great database on
15:41 * pyrimidine goes to a meeting
15:43 * Ultini wanders off
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15:51 * dbolser stares at rbuels
15:54 rbuels eh? what?
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16:59 * deafferret stares at rbuels
17:00 * deafferret notices phant staring at rbuels
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17:38 dbolser $intensity <=> $prev_intensity || $prev_intensity; # ;D
17:39 dbolser perl gets faster with fewer chars right?
18:15 rbuels erm, no.
18:59 deafferret yes it does!  time perl -e 1   0.057s   time prl -e 1   0.019s    3 times faster!
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19:30 josh_ Hello all, I have a quick bioperl question.
19:31 josh_ I'm writing a script that grabs two genes from a couple contig sequences.  I have the gene positions, so its pretty easy for me to use the "$seq->trunc(position1,position2)" function to get the genes
19:32 josh_ I'm passing that truncated sequence directly to my seqIO object, which writes it to the file.
19:34 josh_ however, the sequence still has the name of the contig when its written out.  I was wondering if there was a way to change it while making that function call... i.e. its like "$seqIO_object->write_seq($seq​->trunc(position1,position2))
19:35 josh_ which looks so nice... and I don't want to break up the line of code. this is mainly vanity right now.  But it there is a way to do it, I'd be quite interested.
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19:40 barva does anyone know how to make a Tk::Scrolled autoscroll to the bottom?
19:40 perl_splut no way that I can think of, josh_
19:41 barva $textbox = $mw -> Scrolled ('ROText',-scrollbars => 'oe');
19:41 barva this would be the widget
19:41 josh_ That's too bad, I was sort of hoping there was a hidden flag in the trunc or the write_seq  functions that let you specify what the id would be written out
19:42 perl_splut if they are contigs, are they composed of Bio::SeqFeature::Generic objects inside?
19:43 josh_ well, they are all sequences being read in from a multifasta file.  basically raw output from our 454 sequencer.  Unfortunately, I'm relatively new to bioperl, so I don't know the object structures very well
19:43 barva there should be a command, but I cannot find anything on cpan...
19:45 josh_ I just use the Bio::SeqIO->new( -format='fasta', -file='filename.fasta') to read it in
19:46 perl_splut barva, it all depends on the parent widget. Scrolled just adds scrollbars to another widget
19:46 perl_splut so, look at the code for ROText
19:47 perl_splut josh_, probably not then.
19:48 perl_splut so it makes sense that the trunc contains the same name as the parent item it was pulled from
19:48 perl_splut you'll need to overwrite the display_id once trunc returns a Bio::Seq object
19:48 perl_splut then write that out
19:49 perl_splut barva: http://tech.groups.yahoo.c​om/group/ptk/message/9408
19:53 josh_ Yep, thanks perl_splut.  Its all set up now.
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